Acta crystallographica. Section F, Structural biology communications最新文献_第2页

Crystal structure of the NKX2-1 homeodomain bound to a palindromic DNA recognition sequence NKX2-1同位结构域与回文DNA识别序列结合的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-08-28 Epub Date: 2026-08-07 DOI: 10.1107/S2053230X26007466

Aiswarya Mohandas, Hyun-Joo Nam

引用次数: 0

Structural and functional analysis of peptidyl-tRNA hydrolase 2 from Candidatus Lokiarchaeum sp. GC14_75 候选菌GC14_75肽基trna水解酶2的结构与功能分析

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-08-28 Epub Date: 2026-08-21 DOI: 10.1107/S2053230X26008423

Aoi Kawashima, Kosuke Ito

{"title":"Structural and functional analysis of peptidyl-tRNA hydrolase 2 from Candidatus Lokiarchaeum sp. GC14_75","authors":"Aoi Kawashima, Kosuke Ito","doi":"10.1107/S2053230X26008423","DOIUrl":"10.1107/S2053230X26008423","url":null,"abstract":"Peptidyl-tRNA hydrolase (Pth2) hydrolyzes peptidyl-tRNA, an immature product of aborted translation, into peptide and tRNA, thereby maintaining cellular protein synthesis through peptide release and tRNA recycling. Here, we present the crystal structure of Pth2 from Candidatus Lokiarchaeum sp. GC14_75 (LokiPth2) at 2.12 Å resolution. This is the first structure of Pth2 from a lineage within Promethearchaeati, a kingdom of archaea closely related to eukaryotes. The structure reveals that LokiPth2 forms a homodimer and closely resembles Pth2 structures from other species. However, LokiPth2 exhibits two prominent structural differences: a short helix around the catalytic center, which is absent in other Pth2s, and a distinct orientation of the C-terminal helix. Detailed comparative structural analysis suggests that these regions may regulate enzymatic activity and substrate binding, respectively. Furthermore, the corresponding regions in other Pth2s also exhibit high flexibility, suggesting that similar mechanisms may be conserved among Pth2s. To gain insights into the growth environment of Candidatus Lokiarchaeum sp. GC14_75, we assess the optimal temperature for the catalytic reaction of LokiPth2, which suggests that Candidatus Lokiarchaeum sp. GC14_75 inhabits moderately thermophilic environments.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 9","pages":"320-328"},"PeriodicalIF":1.1,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-08-17

引用次数: 0

Crystal structure of Legionella pneumophila glycosidase effector LegY 嗜肺军团菌糖苷酶效应器LegY的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-08-03 Epub Date: 2026-07-10 DOI: 10.1107/S2053230X26006485

Jing Chen, Fan Li, Shao-Yuan Wang, Tao-Tao Chen

{"title":"Crystal structure of Legionella pneumophila glycosidase effector LegY","authors":"Jing Chen, Fan Li, Shao-Yuan Wang, Tao-Tao Chen","doi":"10.1107/S2053230X26006485","DOIUrl":"10.1107/S2053230X26006485","url":null,"abstract":"Legionella pneumophila translocates approximately 330 effectors into host cells via its type IVB secretion system. These effectors mediate a diverse array of post-translational modifications, among which reversible glycosylation is closely associated with bacterial virulence. Although several glycosyltransferase effectors have been identified that glycosylate host proteins to subvert host cellular processes, no glycosidase effector has been reported to date. Here, we report the crystal structure of LegY, a putative glycosidase effector from L. pneumophila, determined to 1.46 Å resolution (PDB entry 27xj). LegY adopts a single-domain (α/α)6-barrel fold and is structurally assigned as a member of glycoside hydrolase family 15 (GH15). LegY structurally shows high similarity to fungal glucoamylases but shares lower homology with known prokaryotic counterparts. Phylogenetic analysis clusters LegY within the fungal clade, suggesting possible horizontal gene transfer or convergent evolution. This study provides structural insights into LegY, laying a foundation for future uncovering of its putative function during L. pneumophila infection.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 8","pages":"264-274"},"PeriodicalIF":1.1,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148417894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

WebCalEM: a browser-based tool for routine and accurate pixel-size calibration in cryo-EM WebCalEM：一个基于浏览器的工具，用于常规和精确的低温电镜像素尺寸校准。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-08-03 DOI: 10.1107/S2053230X26006308

Lan Dang, Zhiqing Wang, Sung Hyun (Joseph) Cho, Siduo Li, Geetanjali Chakraborty, Nahian Fyrose Fahim, Wen Jiang

{"title":"WebCalEM: a browser-based tool for routine and accurate pixel-size calibration in cryo-EM","authors":"Lan Dang, Zhiqing Wang, Sung Hyun (Joseph) Cho, Siduo Li, Geetanjali Chakraborty, Nahian Fyrose Fahim, Wen Jiang","doi":"10.1107/S2053230X26006308","DOIUrl":"10.1107/S2053230X26006308","url":null,"abstract":"Accurate determination of the image pixel size is critical for quantitative cryo-electron microscopy analyses, yet existing calibration methods remain under-utilized because installation barriers and workflow complexity discourage routine adoption. To fill in this gap, a web-based application, WebCalEM, was developed to transform specialized calibration procedures into an accessible routine practice. Micrographs of any specimen with a known crystalline lattice, such as gold or graphene oxide, are uploaded through a standard browser, processed entirely client-side and analyzed with real-time visualization and downloadable statistical outputs. The application is delivered as a single self-contained HTML file that runs in any modern web browser without server-side computation, a configuration that is well suited to isolated core-facility microscope workstations. Cross-standard consistency between gold and graphene oxide measurements across two microscopes and ten magnification settings yields a Bland–Altman bias of −0.005% of nominal with 95% limits of agreement of [−0.30%, +0.29%]. By delivering this workflow with no local installation, WebCalEM lowers the practical barrier to documented per-dataset magnification calibration in routine cryo-EM operation.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 8","pages":"283-288"},"PeriodicalIF":1.1,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of human aldehyde oxidase under tris(2-carboxyethyl)phosphine reducing conditions 三（2-羧乙基）膦还原条件下人醛氧化酶的结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-08-03 DOI: 10.1107/S2053230X26006904

Carolina Videira, Mariam Esmaeeli, Silke Leimkühler, Maria João Romão, Cristiano Mota

{"title":"Structure of human aldehyde oxidase under tris(2-carboxyethyl)phosphine reducing conditions","authors":"Carolina Videira, Mariam Esmaeeli, Silke Leimkühler, Maria João Romão, Cristiano Mota","doi":"10.1107/S2053230X26006904","DOIUrl":"10.1107/S2053230X26006904","url":null,"abstract":"The importance of human aldehyde oxidase (hAOX1) has increased in recent decades due to its involvement in drug metabolism. Inhibition studies involving hAOX1 are extensive and a common reducing agent, dithiothreitol (DTT), was recently found to inactivate the enzyme. However, in previous crystallographic studies of hAOX1, DTT was found to be essential for crystallization. To surpass this concern, another reducing agent was used in crystallization trials. Using tris(2-carboxyethyl)phosphine (TCEP), a sulfur-free reducing agent, it was possible to obtain well ordered crystals of wild-type hAOX1 and a variant, hAOX1_6A, which diffracted beyond 2.3 Å resolution. Instead of the typical star-shaped crystals of hAOX1, at pH 4.7 plates are obtained in the orthorhombic space group P21212 with two molecules in the asymmetric unit. Activity assays with the enzyme incubated with both reducing agents show that in contrast to DTT, TCEP did not inactivate hAOX1. The replacement of DTT with TCEP in the crystallization of hAOX1 provides a strategy to circumvent enzyme inactivation during crystallographic studies, allowing future applications of new assays, such as time-resolved crystallography.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 8","pages":"275-282"},"PeriodicalIF":1.1,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148590171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Show me how it's done: introducing Protocols 告诉我怎么做：介绍协议。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-08-03 DOI: 10.1107/S2053230X26006965

Dorothee Liebschner, Michael A. Hough, Stephen P. Muench, Kyeong Kyu Kim, Mark J. van Raaij, Maria Cristina Nonato, Jon Agirre

引用次数: 0

Crystal structure of the type VI secretion system adaptor protein Tla3 from Pseudomonas aeruginosa 铜绿假单胞菌VI型分泌系统接头蛋白Tla3的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-07-07 Epub Date: 2026-06-13 DOI: 10.1107/S2053230X26005765

Bidisha Chakraborty, Saumen Datta

{"title":"Crystal structure of the type VI secretion system adaptor protein Tla3 from Pseudomonas aeruginosa","authors":"Bidisha Chakraborty, Saumen Datta","doi":"10.1107/S2053230X26005765","DOIUrl":"10.1107/S2053230X26005765","url":null,"abstract":"The type VI secretion system (T6SS) is a dynamic protein nanomachine employed by Gram-negative bacteria to secrete toxic effector proteins directly into microbial competitors, eukaryotic host cells, or the environment. The T6SS is primarily involved in interbacterial antagonism, along with host-cell manipulation and resource scavenging, underscoring its central role in microbial community structuring and establishment of infection. Pseudomonas aeruginosa employs the 52 kDa adaptor protein Tla3 for the successful loading of the antibacterial phospholipase effector Tle3 onto the H2-T6SS machinery. Tla3 is reported to contain two DUF2875 domains. To date, no structural information is present for DUF2875 domain-containing adaptor proteins of the T6SS. Here, we report the 1.8 Å resolution crystal structure of the T6SS adaptor protein Tla3 from P. aeruginosa strain UCBPP-PA14. The structure shows a thiolase-like fold, with a conserved five-layered α–β–α–β–α core topology. Detailed atomic insight into the structure is significant, as it adds to the hitherto limited structural knowledge of adaptor-mediated effector-loading mechanisms in the T6SS, thereby contributing to a broader understanding of T6SS functionality.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 7","pages":"237-244"},"PeriodicalIF":1.1,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148248814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure of human Dickkopf 4 cysteine-rich domain 1 and evaluation of conformational rigidity 人dickkopf4半胱氨酸富结构域1的晶体结构及构象刚性评价。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-07-07 Epub Date: 2026-06-22 DOI: 10.1107/S2053230X26006333

Naoki Shibata

{"title":"Crystal structure of human Dickkopf 4 cysteine-rich domain 1 and evaluation of conformational rigidity","authors":"Naoki Shibata","doi":"10.1107/S2053230X26006333","DOIUrl":"10.1107/S2053230X26006333","url":null,"abstract":"Dickkopf (DKK) family proteins (DKK1–DKK4), which function as extracellular modulators of Wnt signaling, contain two cysteine-rich domains: CRD1 and CRD2. In DKK1, CRD1 modulates interaction with its receptor low-density lipoprotein receptor-related protein (LRP) 5/6, whereas CRD2 directly binds to LRP5/6. The crystal structure of human DKK4-CRD1 was determined at 1.83 Å resolution. Crystals were obtained from refolded protein expressed as inclusion bodies and belonged to space group P21, with two molecules in the asymmetric unit. Initial molecular-replacement attempts using the solution NMR structure were unsuccessful, whereas an AlphaFold2-predicted model provided a clear solution. The refined structure reveals a compact fold comprising N- and C-subdomains connected by a linker region and stabilized by five conserved disulfide bonds. The crystal structure closely resembles the AlphaFold2 model, but shows larger deviations from the NMR ensemble. ANSURR analysis and hydrogen-bond comparisons indicate that the NMR models underestimate structural rigidity, particularly in β-sheet regions, owing to fewer stabilizing hydrogen bonds. Notably, enhanced conformational variability is observed in the N-subdomain, suggesting a potential role for structural plasticity in ligand recognition.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 7","pages":"245-251"},"PeriodicalIF":1.1,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148292995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure of the cytosolic Nudix-like domain of CD-NTase-associated protein 16 from Enterococcus faecalis 粪肠球菌cd - nase相关蛋白16细胞质内nudix样结构域的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-07-07 Epub Date: 2026-06-04 DOI: 10.1107/S2053230X26005285

Tinashe Makanyire, Zihan Zhou, Wanqian Wu, Mingyan Li, Shenglan Xia, HaoYuan Shi, Jianping Kong, Zhaoxing Li, Yibei Xiao

{"title":"Crystal structure of the cytosolic Nudix-like domain of CD-NTase-associated protein 16 from Enterococcus faecalis","authors":"Tinashe Makanyire, Zihan Zhou, Wanqian Wu, Mingyan Li, Shenglan Xia, HaoYuan Shi, Jianping Kong, Zhaoxing Li, Yibei Xiao","doi":"10.1107/S2053230X26005285","DOIUrl":"10.1107/S2053230X26005285","url":null,"abstract":"The cyclic oligonucleotide-based antiphage signaling system (CBASS) employs diverse effector proteins to trigger abortive infection upon phage invasion, yet structural information on membrane-associated CBASS effectors remains limited. CD-NTase-associated protein 16 from Enterococcus faecalis (EfCap16) is a predicted CBASS effector comprising an N-terminal transmembrane region and a C-terminal Nudix-like domain. Here, we report the recombinant expression, purification, crystallization and X-ray crystal structure of the cytosolic Nudix domain of EfCap16 (PDB entry 22lg) in space group P1211. The protein was purified to homogeneity and crystallized, and its structure was determined at 1.6 Å resolution. The EfCap16 Nudix domain shares structural similarity with the Nudix superfamily and contains a conserved Nudix motif. This structure provides a reference framework for future biochemical and functional studies of transmembrane CBASS effectors.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 7","pages":"231-236"},"PeriodicalIF":1.1,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148154706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0